JAL-629 Add some shortnames to args. Add Opt.OUTPUT and allow --output=*.ext to be...

[jalview.git] / help / help / helpTOC.xml

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 1b4156e..11f0541 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -29,7 +29,7 @@
                                <tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
                                <tocitem text="Startup Memory Settings" target="startupprefs" />
                        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
-                       <tocitem text="Command line launch scripts" target="jalviewcltool"/>
+                       <tocitem text="Command line launch" target="jalviewcltool"/>
                </tocitem>
                
                <tocitem text="Editing Alignments" target="edit" />
@@ -90,16 +90,17 @@
                        <tocitem text="ClustalX" target="colours.clustal" />
                        <tocitem text="Zappo" target="colours.zappo" />
                        <tocitem text="Taylor" target="colours.taylor" />
-                       <tocitem text="gecos:flower" target="colours.gecos-flower" />
-                       <tocitem text="gecos:blossom" target="colours.gecos-blossom" />
-                       <tocitem text="gecos:sunset" target="colours.gecos-sunset" />
-                       <tocitem text="gecos:ocean" target="colours.gecos-ocean" />
+                       <tocitem text="gecos Flower" target="colours.gecos-flower" />
+                       <tocitem text="gecos Blossom" target="colours.gecos-blossom" />
+                       <tocitem text="gecos Sunset" target="colours.gecos-sunset" />
+                       <tocitem text="gecos Ocean" target="colours.gecos-ocean" />
                        <tocitem text="Hydrophobicity" target="colours.hydro" />
                        <tocitem text="Helix propensity" target="colours.helix" />
                        <tocitem text="Strand propensity" target="colours.strand" />
                        <tocitem text="Turn propensity" target="colours.turn" />
                        <tocitem text="Buried index" target="colours.buried" />
                        <tocitem text="Nucleotide colours" target="colours.nucleotide" />
+                       <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
                        <tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
                        <tocitem text="Blosum62" target="colours.blosum" />
                        <tocitem text="by Percentage Identity" target="colours.pid" />